rs12962411

chr18-31811560-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.071 in 152,202 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10804 AN: 152084 Hom.: 402 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0791

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0710 AC: 10807 AN: 152202 Hom.: 401 Cov.: 32 AF XY: 0.0704 AC XY: 5242 AN XY: 74430

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.0640

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0545

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.0723

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0798 Hom.: 703

Bravo AF: 0.0708

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.0
Dann	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12962411; hg19: chr18-29391523;